title: DNA methylation patterns in CD8+ T cells discern psoriasis from psoriatic arthritis and correlate with cutaneous disease activity

status: Public on Sep 22 2021

city: Liverpool

first: Christian

last: Hedrich

state: Please select...

address: Department of Women's & Children's Health,University of Liverpool, Alder Hey Children's NHS Foundation Trust,Eaton Road,

type: Methylation profiling by genome tiling array

summary:
Background: Psoriasis is a T cell-mediated chronic autoimmune/inflammatory disease. While some patients experience disease limited to the skin (skin psoriasis), others develop joint involvement (psoriatic arthritis; PsA). In the absence of disease- and/or outcome-specific biomarkers, and as arthritis can precede skin manifestations, diagnostic and therapeutic delays are common and contribute to disease burden and damage accrual.
Objective: Altered epigenetic marks, including DNA methylation, contribute to effector T cell phenotypes and altered cytokine expression in autoimmune/inflammatory diseases. This project aimed at the identification of disease-/outcome-specific DNA methylation signatures in CD8+ T cells from patients with psoriasis and PsA as compared to heathy controls.
Method: Peripheral blood CD8+ T cells from 9 healthy controls, 10 psoriasis and 7 PsA patients were collected to analyze DNA methylation marks using Illumina Human Methylation EPIC BeadChips (>850,000 CpGs per sample). Bioinformatic analysis was performed using R (minfi, limma, ChAMP and DMRcate packages).
Results:  DNA methylation profiles in CD8+ T cells differentiate healthy controls from psoriasis patients (397 Differentially Methylated Positions (DMPs); 9 Differentially Methylated Regions (DMRs) when ≥CpGs per DMR were considered; 2 DMRs for ≥10 CpGs). Furthermore, patients with skin psoriasis can be discriminated from PsA patients (1861 DMPs, 20 DMRs (≥5 CpGs per region), 4 DMRs (≥10 CpGs per region)). Gene ontology (GO) analyses considering genes with ≥1 DMP in their promoter delivered methylation defects in skin psoriasis and PsA primarily affecting the BMP signaling pathway and endopeptidase regulator activity, respectively. GO analysis of genes associated with DMRs between skin psoriasis and PsA demonstrated an enrichment of GABAergic neuron and cortex neuron development pathways. Treatment with cytokine blockers associated with DNA methylation changes (2372 DMPs; 1907 DMPs within promoters, 7 DMRs (≥5CpG per regions)) affecting transforming growth factor beta receptor and transmembrane receptor protein serine/threonine kinase signaling pathways. Lastly, a methylation score including TNF and IL-17 pathway associated DMPs inverse correlates with skin disease activity scores (PASI).
Conclusion: Patients with skin psoriasis exhibit DNA methylation patterns in CD8+ T cells that allow differentiation from PsA patients and healthy individuals, and reflect clinical activity of skin disease. Thus, DNA methylation profiling promises potential as diagnostic and prognostic tool to be used for molecular patient stratification towards individualized treatment.
This project aimed at the identification of disease-/outcome-specific DNA methylation signatures in CD8+ T cells from patients with psoriasis and PsA as compared to heathy controls.

overall_design: Genome wide DNA methylation profiles were analyzed in CD8+T cells from patients with psoriatic arthritis (PsA), skin psoriasis (psoriasis) and healthy control (HC)

first: Amandine

last: Charras

first: Jessica

last: Garau

first: Sigrun

last: Hofmann

first: Emil

last: Carlsson

first: Cristina

last: Cereda

first: Susanne

last: Russ

last: Abraham


city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

country: USA

institute: Tulane Health Sciences Center

summary: RiboMethSeq of HCT116 cells treated with siCoilin to investigate the effect of Coilin knockdown on RNA methylation as part of a larger study on the function of the protein TFIP11.

overall_design: RiboMethSeq of HCT116 cells mock-transfected, transfected with control siRNA, or tranfected with one of two different siCoilin.

first: Denis

last: Mottet

last: Duchemin

last: Lafontaine


title: RNA-Sequencing of cardiac and renal tissues from CLP-induced mice and melatonin-treated mice with CLP

city: Nanjing

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

country: China

institute: Nanjing Medical University

type: Expression profiling by high throughput sequencing

summary: Melatonin (N-acetyl-5-methoxytryptamine) has been shown to have a cardioprotective effect against inflammatory diseases. However, the mechanisms underlying the protective role of melatonin in these diseases remain to be revealed. In this study, melatonin was administrated to mice 14 days before cecal ligation puncture surgery. The characteristics of sepsis-induced AKI and myocarditis were detected. The results showed that melatonin could alleviated cardiac and renal dysfunction in sepsis model. RNA-seq analysis showed that MLT repressed the oxidant stress in response to kidney injury. RNA sequencing assays with heart tissues showed melatonin maintains the mitochondrial function in sepsis-caused myocarditis.

overall_design: Examination of 2 different cardiac and renal  tissues from CLP-induced mice and melatonin-treated mice with CLP

first: Qiulun

last: Lu

first: Liyang

last: Chen


summary: RNA-Seq of HeLa cells treated with siDHX15 or control siRNA to investigate the effect of DHX15 knockdown on mRNA as part of a larger study on the function of TFIP11 and DHX15.

overall_design: 3 replicates of HeLa cells treated with siDHX15, 3 replicates of HeLa cells treated with siGL3 (control).

first: Sarah

last: Hanache


title: Transcriptomic analysis of lung endothelial subsets in experimental sepsis

city: Malmö

first: Milladur

last: Rahman

state: Skane

address: Jan Waldenströmsg. 35 hus 91 plan 10

department: Department of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

summary: Purpose: Sepsis affects almost all aspects of endothelial cell function. Lung endothelial subsets, capillaries (capEC)  and post capillary venules (PCV), are known to play a pivotal role in maintaining normal homeostasis. The aim of the study is to reveal transcriptional changes in lung endothelial subsets during sepsis. Methods: Sepsis was induced in male C57BL/6 mice by cecal ligation and puncture (CLP). Lung tissues were collected 4 hour after induction of sepsis. Single cell suspension was prepared by enzymatic digestion. Blood endothelial cells (BECs) were enriched by depletion of hematolymphoid cells and epithelial cells by using anti-CD45 and CD326 microbeads. CapEC and PCV were sorted from enriched BECs using fluorescent-labeled antibodies. capEC subset was identified as CD31+Icam1+Vcam1- and PCV subset was identified as CD31+Icam1+Vcam1+. EC subsets were directly sorted into RLT buffer. Total RNA was isolated from the sorted cells with RNeasy Plus Micro kit (Qiagen) and the quality of RNA was checked by Bioanalyzer RNA 6000 pico assay. Sequence library was prepared using SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara Bio USA, Inc.). After library preparation and quality check, the double-stranded-cDNA was sequenced on NextSeq 500 (Illumina) using (read one-index reads-read two, bp): 75-8-8-75 setup. Differentially expression analysis was performed using DESeq2 in R program. Results: Differential expression analysis revealed that lung capEC is transcriptionally different than PCV. capEC and PCV responded differently after induction of sepsis. Enrichment analysis revealed that capEC are more enriched with genes related to regulation of coagulation, vascular permeability, wound healing and lipid metabolic process. On the other hand, PCV are more enriched with genes related to cell chemotaxis, cell-cell adhesion by integrins, chemokine biosynthesis process, regulation of actin filament process, neutrophil homeostasis.

overall_design: Abdominal sepsis was induced in C57BL/6 mice by CLP. Lung endothelial cells were sorted for total RNA extraction and transcriptomic analysis.


title: HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1::CLOCK chromatin binding and shaping rhythmic chromatin landscape

status: Public on Sep 23 2021

city: Los Angeles

first: Meng

last: Qu

state: California

address: 1002 West Childs Way

department: Keck Medical School

institute: University of Southern California

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seqs of BMAL1, HNF4A, FOXA2, H3K4me1, and H3K27ac were profiled in mouse liver tissues upon Hnf4a or Bmal1 knockout. BMAL1, H3K4me1, and H3K27ac ChIP-seq were profiled in U2OS cells ectopically expressing HNF4A.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of BMAL1 genome binding and histone modifications distribution in Hnf4a knockout or HNF4A ectopic expression systems.

first: Han

first: Zhenyu

last: Jia

first: Steve

middle: A

last: Kay


title: Pparg drives luminal differentiation and luminal tumor formation in the urothelium

city: New York

first: Cathy

last: Mendelsohn

state: NY

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University

summary: We find that Pparg is a master regulator of cell specification during urothelial homeostasis, driving a luminal differentiation program via retinoid signaling.  Interestingly, expression of activated Pparg in basal cells only drives tumor formation when they are in an activated state, that are in an activated state, induces formation of luminal tumors with papillary morphology, Expression of an activated form of Pparg induces basal cells at homeostasis, to differentiate directly into luminal cells. In a BBN mouse model which produces basal subtypes tumors in wild type animals, activated Pparg drives formation of luminal tumors, suggesting that this transcription factor is a master regulator of luminal differentiation, as has been suggested from in vitro studies.

overall_design: mRNA profiles of WT and K5VP16;Pparg mutant urothelial cells


title: To identify novel targets of Mxr1p in Pichia pastoris cultured in methanol

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

summary: Pichia pastoris (Komagataella phaffi) transcription factor Mxr1p is known to regulate multiple metabolic pathways by binding to Mxr1p response elements of target genes. Mxr1p possesses a transactivation domain within the N-terminal 400 amino acids (Mxr1N400) which is functional during methanol metabolism. (Parua et al; 2012)  Studies from our lab have shown that delta_mxr1 complemented with Mxr1N400 fails to reverse the growth defect of delta_mxr1 cultured in a medium containing methanol suggesting that region beyond N-terminal 400 amino acids has an essential function. We employed DNA microarray to identify genes whose expression is regulated by Mxr1N400 and full length Mxr1 during methanol metabolism.  Pichia pastoris 14-3-3 regulates transcriptional activity of the methanol inducible transcription factor Mxr1 by direct interaction. Pabitra K. Parua, Paul M. Ryan and Elton T. Young. Molecular microbiology, 2012

overall_design: Agilent Pichia Pastoris  8x15k Gene Expression  (AMADID: 085736) designed by Genotypic Technology privatted Limited, Bangalore  ,

first: P

middle: N

last: Rangarajan


type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA-Seq of HeLa cells treated with siTFIP11 or control siRNA to investigate the effect of TFIP11 knockdown on small RNA (snRNA, snoRNA, etc.) as part of a larger study on the function of TFIP11.

overall_design: 3 replicates of HeLa cells treated with siTFIP11, 3 replicates of HeLa cells treated with siGL3 (control).

first: Amandine


summary: RNA-Seq of HeLa cells treated with siTFIP11 or control siRNA to investigate the effect of TFIP11 knockdown on mRNA as part of a larger study on the function of TFIP11.


title: Primary brain cell infection by Toxoplasma gondii reveals the dynamics of spontaneous bradyzoite differentiation and the extend of modification of neuron biology after infection

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

country: France

institute: CNRS

summary: Toxoplasma gondii is a eukaryotic parasite that form latent cyst in the brain of immunocompetent individuals. The latent parasites infection of the immune privileged central nervous system is linked to most complications. With no drug currently available to eliminate the latent cysts in the brain of infected hosts, the consequences of neurons long-term infection are unknown.. It has long been known that T. gondii specifically differentiate into a latent form (bradyzoite) in neurons, but how the infected neuron is responding to the infection remain to be elucidated. We have established a new in vitro model resulting in the production of fully mature bradyzoites cysts in brain cells. Using dual, host and parasite, RNA-seq we characterized the dynamics of differentiation of the parasite, revealing the involvement of key pathways in this process. Moreover, we identified how the infected brain cells responded to the parasite infection revealing the drastic changes that take place. We showed that neuronal specific pathways are strongly affected, with synapse signaling being particularly affected, especially glutamatergic synapse. The establishment of this new in vitro model allows to investigate both the dynamics of the parasite differentiation and the specific response of neurons to the long term infection by this parasite.

sample_organism:
Toxoplasma gondii
Rattus norvegicus

platform_organism:
Toxoplasma gondii
Rattus norvegicus

overall_design: Three biological replicate of the mutant strain in presence and in abscence of Auxin. mRNA profiles  iKD TgAP2IX-5 parasites was generated by high throughput sequencing using HiSeq 2500 system (Illumina).

first: Thomas

last: Mouveaux

first: Ludovic

last: Huot


title: RybB-mRNA pairing in absence of the RNA chaperone Hfq in vivo

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

country: Canada

institute: University of Sherbrooke

summary: The RNA chaperone Hfq is regarded as a critical effector promoting interaction between small regulatory RNAs (sRNAs) and cognate target mRNAs. While much of this interpretation is based on in vitro assays, no in vivo evidence actually exists to support this model. Here we report that Hfq is typically unnecessary for binding of various sRNA-mRNA complexes in vivo. Data obtained from pull-downs of MS2-tagged RyhB, RybB and DsrA sRNAs followed by RNAseq identification of target mRNAs suggest that absence of Hfq is not essential for sRNA-mRNA complex formation in vivo.

overall_design: Identification of RNAs co-purified with MS2-RybB in Δhfq ΔrybB background.

first: David

last: Lalaouna


title: RyhB-mRNA pairing in absence of the RNA chaperone Hfq in vivo

overall_design: Identification of RNAs co-purified with MS2-RyhB in Δhfq ΔryhB background.


title: sRNA-mRNA pairing in absence of the RNA chaperone Hfq

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: DsrA-mRNA pairing in absence of the RNA chaperone Hfq in vivo

overall_design: Identification of RNAs co-purified with MS2-DsrA in Δhfq ΔdsrA background.


title: Degradome-seq of maize

status: Public on Sep 21 2021

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

summary: Degradome-seq of maize

overall_design: The degradome-seq library were constructed based on a previously described method (Zhai et al., 2014)

first: Juan

last: He


title: A novel microglial transcription profile is driven by sex and APOE4 interactions in both mouse and human models of Alzheimer’s disease

first: Michael

last: Workman

state: CA

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

summary: Using a transgenic mouse model of AD that expresses human APOE, we identify a unique transcriptional profile associated with APOE4 expression. We also show a sex and APOE interaction, such that both female sex and APOE4 drive expression of this gene profile. We then confirm these findings in human cells, using microglia derived from induced pluripotent stem cells.

overall_design: Bulk RNA-seq profiles of microglia sorted from mice carrying human APOE (introduced by targeted replacement) on control or 5xFAD genetic background and human microglia differentiated from induced pluripotent stem cells derived from healthy control patients genotyped for APOE +/- heavy metal treatment

middle: J

first: V

last: Moser

first: Clive

last: Svendsen


title: Resolving multiple epigenetic barriers to pig SCNT-mediated reprogramming during embryonic genome activation [RNA-Seq]

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

summary: Pig cloning by somatic cell nuclear transfer (SCNT) frequently undergoes incomplete epigenetic remodeling during the maternal-to-zygotic transition, which leads to a significant embryonic loss before implantation. Here, we generated the first genome-wide landscapes of histone methylation in pig SCNT embryos. Excessive H3K9me3 and H3K27me3, but not H3K4me3, were observed in the genomic regions with unfaithful embryonic genome activation and donor cell-specific gene silencing. A combination of H3K9 demethylase KDM4A and GSK126, an inhibitor of H3K27me3 writer, could remove these epigenetic barriers and restore the global transcriptome in SCNT embryos. More importantly, TDG was defined as a pig-specific epigenetic regulator for nuclear reprogramming, which was not reactivated by H3K9me3 and H3K27me3 removal. Both combined treatment and transient TDG overexpression could promote DNA demethylation and enhance the blastocyst forming rates of SCNT embryos, which offers valuable methods to increase the cloning efficiency of genome-edited pigs for agricultural and biomedical purposes.

overall_design: RNA-seq profiles of pig four- to eight-cell SCNT embryos and pig fetal fibroblasts.

first: Xin

last: Liu

first: Lu

last: Chen

first: Tao

last: Wang

first: Zhekun

last: Li

first: Guowei

last: Bu

first: Jingjing

first: Danya

last: Wu

first: Zhen-Xia

first: Yi-Liang

last: Miao


title: The RNA-binding protein HuR is required for antigen-specific germinal centre B cell selection.

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

institute: INSERM

summary: The germinal centre (GC) is a hallmark of adaptive immunity. Gene expression in GCs is tightly regulated but the impact of post-transcriptional mechanisms are largely unknown. Here we show that expression of the RNA binding protein HuR is essential in GCs. In its absence, GC B cells are at a competitive disadvantage and high-affinity antibody production is severely impaired. Mechanistically, HuR affects the transcriptome qualitatively and quantitatively to enable the expression of a Myc- dependent transcriptional program essential for light zone B cells to re-enter into the dark zone for further proliferation and Ig somatic hypermutation. HuR controls the splicing and abundance of mRNAs required for entry into and transition through the S phase of the cell cycle. HuR modulates a gene signature associated with DNA deamination preserving GC B cells from extensive DNA damage and cell death.

overall_design: Germinal centre B cells from the dark zone (DZ, CD19+ IgD- CD38- CD95+ CXCR4+ CD86- cells) and the light zone (LZ, CD19+ IgD- CD38- CD95+ CXCR4- CD86+ cells) were sorted (by FACs) from HuRfl/fl (control) or HuRfl/fl AIDCre (HuR KO) mice at day 7 after immunization with NP-KLH in alum.

last: Diaz-Muñoz

first: Ines

middle: C

last: Osma-Garcia

first: Dunja

last: Capitan-Sobrino

first: Mailys

last: Mouysset

first: Sarah

middle: E

last: Bell

last: Lebeurrier

first: Martin

last: Turner


title: RNAseq of pedriatic IBD and XIAP-deficient biopsy samples

status: Public on Sep 20 2021

city: Munich

first: Monica

last: Yabal

address: Ismaninger straße 22

country: Germany

institute: Technical University of Munich

summary: Deficiency in the X-linked inhibitor of apoptosis protein (XIAP) is the cause for the X-linked lymphoproliferative syndrome 2 (XLP2). About one third of all patients suffers from severe and therapy refractory inflammatory bowel disease (IBD), but the exact pathogenesis remains undefined. We examined the differences in gene expression of pediatric XLP2 patients with IBD to healthy controls and  pediatric IBD patients.

overall_design: RNA was isolated from patient FFPE samples and subjected to RNAseq

first: Thomas

last: Engleitner


title: Resolving multiple epigenetic barriers to pig SCNT-mediated reprogramming during embryonic genome activation

first: Jing-Jing

last: Zhang

type: Methylation profiling by high throughput sequencing

summary:
Pig cloning by somatic cell nuclear transfer (SCNT) frequently undergoes incomplete epigenetic remodeling during the maternal-to-zygotic transition, which leads to a significant embryonic loss before implantation. Here, we generated the first genome-wide landscapes of histone methylation in pig SCNT embryos. Excessive H3K9me3 and H3K27me3, but not H3K4me3, were observed in the genomic regions with unfaithful embryonic genome activation and donor cell-specific gene silencing. A combination of H3K9 demethylase KDM4A and GSK126, an inhibitor of H3K27me3 writer, could remove these epigenetic barriers and restore the global transcriptome in SCNT embryos. More importantly, TDG was defined as a pig-specific epigenetic regulator for nuclear reprogramming, which was not reactivated by H3K9me3 and H3K27me3 removal. Both combined treatment and transient TDG overexpression could promote DNA demethylation and enhance the blastocyst forming rates of SCNT embryos, which offers valuable methods to increase the cloning efficiency of genome-edited pigs for agricultural and biomedical purposes.

This SuperSeries is composed of the SubSeries listed below.


title: Resolving multiple epigenetic barriers to pig SCNT-mediated reprogramming during embryonic genome activation [ChIP-Seq]

overall_design: Examination of histone H3K4me3, H3K9me3, H3K27me3 modifications in pig 4-cell SCNT embryos and pig fetal fibroblasts.

first: Xin

last: Liu

first: Lu

last: Chen


title: Epromoters function as a hub to recruit key transcription factors required for the interferon/inflammatory response

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

summary: Gene expression is controlled by the involvement of gene-proximal (promoters) and distal (enhancers) regulatory elements. Previous results have demonstrated that a subset of gene promoters, also termed Epromoters, works as bona fide enhancers and regulate distal gene expression. We hypothesised that Epromoters might play a key role in the coordination of rapid gene induction in the stress response, in particular during inflammation. Using a high-throughput reporter assay we explored the function of Epromoter in response to type I interferon. We found that STAT1/2 and IRF transcription factors preferentially bind to IFNa-induced Epromoters and distally regulate the activation of interferon-response genes. Similar observations were made in other types of inflammatory response. Our findings suggest that Epromoters might function as a hub to recruit key TFs required for coordinated regulation of gene clusters during the inflammatory response, and more generally upon cellular response to intra- and extra-cellular signals.

overall_design: Genome-wide analysis via ChIP-Seq for H3K27ac, H3k4me3 AND H3k4me1 in K562 cells stimulated with Interferon alpha for 6 hours and non stimulated; and IRF9 in K562 cells stimulated with interferon alpha for 6 hours; and, CapSTARR-seq using our ref-seq promoter library in K562 cells stimulated with IFNa for 6 hours.

first: David

last: Santiago-Algarra

first: Himanshu

last: Singh

first: Charbel

last: Souaid

first: Lan

middle: T

last: Dao

first: Nori

last: Sadouni

first: Guillaume

last: Charbonnier

first: Spicuglia

last: Salvatore


title: The Clp1 R140H mutation alters tRNA metabolism and mRNA 3’ processing in mouse models of pontocerebellar hypoplasia

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: Homozygous mutation of the RNA kinase CLP1 causes pontocerebellar hypoplasia type 10 (PCH10), a pediatric neurodegenerative disease. CLP1 is associated with the tRNA splicing endonuclease complex and the cleavage and polyadenylation machinery, but its function remains unclear. We generated two mouse models of PCH10: one homozygous for the disease-associated Clp1 mutation, R140H, and one heterozygous for this mutation and a null allele. Both models exhibit loss of lower motor neurons and neurons of the deep cerebellar nuclei. To explore whether Clp1 mutation impacts tRNA splicing, we profiled the products of intron-containing tRNA genes. While mature tRNAs were expressed at normal levels in mutant mice, numerous other products of intron-containing tRNA genes were dysregulated, with pre-tRNAs, introns, and certain tRNA fragments upregulated, and other fragments downregulated. However, the spatiotemporal patterns of dysregulation did not support a role in pathogenicity for most altered tRNA products. To elucidate the effect of Clp1 mutation on pre-mRNA cleavage, we analyzed poly(A) site (PAS) usage and gene expression in Clp1R140H/- spinal cord. PAS usage was shifted from proximal to distal sites in the mutant mouse, particularly in short and closely spaced genes. Many such genes also were expressed at lower levels in the Clp1R140H/- mouse, possibly as a result of impaired transcript maturation. These findings are consistent with the hypothesis that select genes are particularly dependent upon CLP1 for proper pre-mRNA cleavage, suggesting that the contribution of mRNA 3’ processing to pathogenesis in PCH10 merits further investigation.

overall_design: A total of 10 samples are analyzed in this study with genotypes of either Clp1+/+ or Clp1R140H/- in the context of C57BL/6J mice. Motor neurons from two samples of each genotype in P0/P1 mice were isolated from Hlxb9-GFP mice through FACS isolation and 3’READS+ libraries were generated. Additionally, spinal cord from each genotype in P14 mice were used to generate polyA(+) selected RNA-seq libraries for 3 samples in each genotype.

first: Caitlin

last: Monaghan

middle: I

first: Mridu

last: Kapur

first: Jeffrey

middle: H

last: Chuang

first: Susan

middle: L

last: Ackerman


title: Resolving multiple epigenetic barriers to pig SCNT-mediated reprogramming during embryonic genome activation [BiSulfite-seq]

overall_design: Examination of DNA methylation levels in pig 4-cell SCNT embryos and pig fetal fibroblasts.

first: Tao

last: Wang

first: Zhekun

last: Li

first: Guowei

last: Bu

first: Jingjing

first: Danya

last: Wu

first: Zhen-Xia

first: Yi-Liang

last: Miao


first: Tina

last: O'Grady

summary: RiboMethSeq of HCT116 cells treated with siTFIP11 or siDHX15 to investigate the effect of TFIP11 or DHX15 knockdown on RNA methylation as part of a larger study on the function of TFIP11.

overall_design: RiboMethSeq of HCT116 cells mock-transfected, transfected with control siRNA, transfected with one of two different siTFIP11, or tranfected with one of two different siDHX15.

first: Denis

last: Mottet

first: Amandine

last: Duchemin

last: Lafontaine


title: Time series (T= 0-4 hours) for E. coli K-12 MC4100 after a shift from 23˚C to 37˚C (M9 minimal glycerol medium, exponential phase growth)

status: Public on Sep 19 2021

city: Northampton

first: Christine

middle: Ann

last: White-Ziegler

state: MA

address: Clark Science Center

department: Biological Sciences

institute: Smith College

summary: We investigated the effect of a temperature shift from 23˚C to 37˚C, mimicking the temperature transition experienced by a microbe as it enters a human host.  This strategy allowed the exploration of the kinetics of gene expression changes in immediate response to a temperature upshift and to characterize the suite of genes required to respond to 37˚C in the first few hours.  We demonstrate that a significant number of genes are rapidly altered in expression within minutes to hours after a temperature shift.  Some are only induced transiently, while are required for long-term adaptation.  Many of these genes are related to metabolism, stress response, and immune evasion suggesting that temperature may serve as a sentinel cue to predict and prepare for niche adaptation in the host.

overall_design: An aerobic, mid-exponential phase (A600= 0.2-0.6) culture was grown at 23˚C in M9 minimal medium containing glycerol as a carbon source.  Aliquots of the initial culture were shifted to 37˚C to allow harvest of cells at time points after a shift to 37˚C.  Microarray results compare each timepoint after the shift to 37˚C (T= 0.5, 1, or 4 hours) to the initial T=0 timepoint grown at 23˚C.


title: RNA-sequencing of D2A1 and D2.OR cell lines in both 2D and 3D cultures

city: L'Hospitalet de Llobregat

first: Xavier

last: Solé

address: Av. Gran Via 199-203

department: Oncology Data Analytics Program

country: Spain

institute: Catalan Institute of Oncology

summary: Reactivation of dormant cancer cells can lead to cancer relapse, metastasis and patient death. Dormancy is a non-proliferative state and is linked to late relapse and death. No targeted therapy is currently available to eliminate dormant cells, highlighting the need for a deeper understanding and reliable models. Here, we thoroughly characterize the dormant D2.OR and proliferative D2A1 breast cancer cell line models in vivo and in vitro, and assess if there is overlap between a dormant and a senescent phenotype. We show that D2.OR but not D2A1 cells become dormant in the liver of an immunocompetent model. In vitro, we show that D2.OR cells are polyploid ER+/Her2+ cells, and in response to a 3D environment are growth arrested in G1, of which a subpopulation resides in a 4NG1 state. The dormancy state is reversible, and not associated with a senescence phenotype. This will aid future research on breast cancer dormancy.

overall_design: mRNA sequencing of D2A1 and D2.OR cell lines cultured in 2D or 3D, 3 for each condition.

first: Laila

last: Ritsma


title: Cell size is a determinant of stem cell potential during aging

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute


title: Transcriptomic effect of retroviral overexpression of PIK3CA-H1047R in breast epithelial MCF10A cells; +/- 500 nM BYL719 as a function of time (48h and 120h).

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: School of Life Sciences, University of Dundee

summary: The aim of this experiment was to evaluate the transcriptomic effects of PI3K pathway hyperactivation vs inhibition, in the context of PIK3CA-H1047R overexpression in MCF10A breast epithelial cells. The cells were processed for RNA sequencing, with the t values from subsequent differential gene expression processing used for gene set enrichment analysis (GSEA) with the MSigDB HALLMARK_PI3K_AKT_MTOR_SIGNALING gene signature. We demonstrate that the HALLMARK_PI3K_AKT_MTOR_SIGNALING gene signature can be used as a transcriptional footprint of PI3K pathway activation: it correctly predicts activation of the pathway in DMSO-treated PIK3CA-H1047R MCF10A cells relative to EV controls; conversely, it also correctly predicts pathway inhibition upon p110 inhibition with BYL719.

overall_design: Transcriptomic data from untransformed, immortalised human breast epithelial MCF10A cells with retrovirally-mediated overexpression of the PIK3CA-H1047R oncogene, alongside the respective empty vector (EV) control cells; assessed in growth factor-replete conditions, with PIK3CA-H1047R also exposed to either DMSO or 500 nM BYL719 (p110alpha-specific inhibitor) in order to determine the extent to which the transcriptomic phenotype can be reversed. Data were obtained from two treatment time points - 48h and 120h. Following differential gene expression analysies with limma-voom, the genes were ranked according to the t values specifying a given comparison, and used to determine whether conventional gene set enrichment analysis (GSEA) with the the mSigDb "HALLMARK_PI3K_AKT_MTORC1" gene signature would distinguish samples with PI3K pathway activation vs inhibition.

middle: R

first: Alex

last: Toker

first: Emily

last: Erickson


title: Cell size is a determinant of stem cell potential during aging (HSC treatments RNA-seq dataset)

summary: Stem cells are remarkably small in size. Human hematopoietic stem cells (HSCs) measure a mere 7 μm in diameter. Whether small size is important for stem cell function is unknown. We find that murine HSCs enlarge under conditions known to decrease stem cell function. This decreased fitness of large HSCs is due to reduced proliferative potential. We further show that preventing HSC enlargement by inhibiting macromolecule biosynthesis or reducing the size of large HSCs by shortening G1 averts the loss of stem cell potential. Naturally large HSCs also exhibit decreased stem cell potential indicating that large size characterizes exhausted HSCs under physiological conditions. Finally, we show that our findings are relevant to aging. A fraction of murine and human HSCs enlarge during aging. Preventing this age-dependent enlargement improves HSC function. We conclude that small cell size is important for stem cell function and propose that stem cell enlargement contributes to their functional decline during aging.

overall_design: Four replicates each of RNA isolated from Hematopoetic Stem Cells isolated from mice treated with vehicle, PD, rapamycin and PD+rapamycin.

first: Jette

last: Lengefeld

first: Chia-Wei

last: Cheng

first: Pema

last: Maretich

first: Marguerite

last: Blair

first: Hannah

last: Hagen

first: Melanie

last: McReynolds

last: Sullivan

first: Kyra

last: Majors

first: Christina

last: Roberts

first: Joon

last: Kang

first: Joachim

last: Steiner

first: Teemu

middle: P

last: Miettinen

first: Scott

last: Manalis

first: Adam

last: Antebi

first: Sean

last: Morrison

first: Jacqueline

last: Lees

first: Laurie

last: Boyer

first: Ömer

last: Yilmaz

first: Angelika

last: Amon


title: Transcriptomic analysis of STAT1/3 in the goat endometrium during embryo implantation

status: Public on Sep 17 2021

city: Yangling

first: Haokun

last: Liu

address: Xinong Road 22

institute: Northwest A&F University

summary:
Purpose: The goals of this study are to compare the differentially expressed genes in IFNT-treated and untreated goat endometrial epithelial cells and screen the signaling pathways related to endometrial receptivity.
Methods: We performed RNA sequencing of goat endometrial epithelial cells (gEECs) with or without 20 ng/mL IFNT treatment. KEGG enrichment analysis was used to screen for enrichment pathways, and qRT-PCR, western blotting and immunohistochemistry were used for in vivo and in vitro validation.
Results: Differential comparison showed that there were 442 upregulated differentially expressed genes (DEGs) and 510 downregulated DEGs. Bioinformatic analyses revealed that DEGs were significantly enriched in immune-related functions or pathways. The results of qRT-PCR, western blotting and immunohistochemistry were consistent with those of RNA-seq.
Conclusion: These results highlight the role of IFNT in regulating endometrial receptivity in gEECs and uncover the temporal and spatial changes in the expression of STAT1/3 during embryo implantation in the goat endometrium.

overall_design: The mRNA profile of goat endometrial epithelial cells with or without 20 ng/mL IFNT treatment were generated by RNA sequencing, in triplicate, using Illumina HiSeq 4000.

first: Caixia

last: Wang

first: Zuhui

last: Li

first: Chunmei

last: Shang

first: Xinyan

last: Zhang

first: Ruixue

first: Aihua

first: Yaping

last: Jin

first: Pengfei

last: Lin


title: Role of TFIP11 in U6 snRNA modification and splicing efficiency

city: New Orleans

first: Tina

last: O'Grady

address: 1430 Tulane Ave., SL79

institute: Tulane Health Sciences Center

overall_design: Refer to individual Series


title: Temperature influences the composition and cytotoxicity of extracellular vesicles in Staphylococcus aureus

city: Athens

first: Paul

last: Briaud

state: OH

address: 107 Irvine Hall

institute: Ohio University

summary: Staphylococcus aureus is a pathogenic bacterium but also a commensal of skin and anterior nares in humans. As S. aureus transits from skins/nares to inside the human body, it experiences changes in temperature. The production and content of S. aureus extracellular vesicles (EV) have been increasingly studied over the past few years and EVs are increasingly being recognized as important to the infectious process. Nonetheless, the impact of temperature variation on S. aureus EVs has not been studied in detail as most reports that investigate EV cargoes and host cell interactions are performed using vesicles produced at 37˚C. Here we report that S. aureus vesicle production is temperature-dependent with greater vesiculation at 40˚C. We demonstrate that the temperature dependent regulation of vesicle production in S. aureus is mediated by the alpha phenol soluble modulin peptides (αPSMs). Through proteomic analysis, we observed increased packaging of virulence factors at 40˚C whereas more total proteins are present in EVs produced at 34˚C. Similar to the protein content, we perform transcriptomic analysis and demonstrate that the RNA cargo is impacted by temperature also. Finally, we demonstrate greater αPSM- and α-toxin mediated erythrocyte lysis with 40˚C EVs but 34˚C EVs are more cytotoxic toward THP-1 cells. Together our study demonstrates that small temperature variations have great impact on EV biogenesis and shape the interaction with host cells.

overall_design: Six data sets in total. Three biological replicates of Extracellular vesicles produced from S. aureus grown at each three temperatures used in the study i.e 34 C, 37 C

first: Andrew

last: Frey

first: Emily

last: Marino

first: Raeven

last: Bastock

first: Richard

last: Wiemels

first: Rebecca

last: Keogh

first: Erin

last: Murphin

first: Lindsey

last: Shaw

first: Ronan

middle: K

last: Carroll


title: Ectopic misexpression of Irx3 and Irx5 in the paraventricular nucleus of the hypothalamus contributes to hyperphagia and neurodevelopmental defects in Sim1 haploinsufficiency

city: Toronto

first: Chi-chung

last: Hui

state: ON

address: 686 Bay street

institute: The Hospital for Sick Children

summary: Single cell sequencing of Sim1-Cre;tdTomato+ FACS sorted cells from hypothalami of wildtype and Sim1 heterozygous mice.

overall_design: Single-cell RNA sequencing (Drop-Seq) was performed on tdTomato+ FACS sorted cells hypohalami of Sim1-Cre;tdTomato and Sim1-Cre;tdTomato;Sim1Het (double-heterozygous) mice at postnatal day 1 to 4. For each genotype, hypothalamus tissues from 6 pups were pooled for single-cell dissociation, followed by FACS sorting and  single-cell RNA sequencing.

first: Joe

last: Son

first: Zhengchao

last: Dou

first: Chi-Chung


title: RNAseq analysis of osteosarcoma cell line with overexpression of YAP-S94A and YAP-S127A

status: Public on Sep 16 2021

city: Nantes

first: Franck

last: Verrecchia

address: 1 Rue Gaston Veil

institute: University of Nantes

summary: The molecular mechanisms by which YAP regulates metastases development were studied using overexpression of mutated forms of YAP able or not to interact with TEAD. Molecular signatures were identified using RNA-sequencing analysis and genes set enrichment.

overall_design: Osteosarcoma cell line KHOS overexpressing two different form of YAP protein : YAP-S94A and YAP-S127A

first: Sarah

last: Morice


title: Immune signatures underlying post-acute COVID-19 lung sequelae

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

summary: Although a substantial proportion of severe COVID-19 pneumonia survivors exhibit long-term pulmonary sequalae, the underlying mechanisms or associated local and systemic immune correlates are not known. Here, we have performed high dimensional characterization of the pathophysiological and immune traits of aged COVID-19 convalescents, and correlated the local and systemic immune profiles with pulmonary function and lung imaging. In this cohort of aged COVID-19 convalescents, chronic lung impairment was accompanied by persistent systemic inflammation and respiratory immune alterations. Detailed evaluation of the lung immune compartment revealed dysregulated respiratory CD8+ T cell responses that likely underlie the impaired lung function following acute COVID-19 during aging. Single cell transcriptomic analysis identified the potential pathogenic subsets of respiratory CD8+ T cells causing persistent tissue conditions following COVID-19. Our results have revealed key pathophysiological and immune traits that support the development of lung sequelae following SARS-CoV2 pneumonia during aging, with implications for the treatment of chronic COVID-19 symptoms.

overall_design: single-cell RNA-seq / TCR-seq assay of PBMC or BAL T cells from aged COVID-19 convalescents or healthy donors

first: Chaofan

last: Li

first: Yue

last: Wu

first: Ying


title: Transcriptome and proteome analysis of the antitumor activity of maslinic acid against pancreatic cancer cells

city: Wenzhou

first: hewei

last: zhang

state: Zhejiang

address: The First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang, Ouhai

summary: Maslinic acid (MA) is a triterpenoid compound of natural abundance in olive plants possessing numerous biological activities. The effect and molecular mechanism of MA on pancreatic cancer cells remain elusive. Here, we explored the anti-tumor activity of MA on human pancreatic cancer cells and the potential underlying molecular mechanism. The anti-cancer effects of MA on whole-cell processes, including proliferation, migration, and invasion in pancreatic cancer cells, were systematically assessed by colony formation, transwell, and migration assays. The search for potential therapeutic targets was achieved via transcriptomics and proteomics analyses. MA was demonstrated to inhibit the proliferation, migration, and invasion of PANC-1 and Patu-8988 cells, but induced apoptosis of these cells. Several key candidate genes and proteins of functional relevance for the anti-tumor activity of MA were identified through the association analysis of transcriptomics and proteomics. To our knowledge, this is the first transcription and proteomics-based comprehensive analysis of the mechanism of MA against pancreatic cancer. The findings demonstrate that MA holds promise as a therapeutic drug for managing pancreatic cancer.

overall_design: PANC-1 cells treated with or without Maslinic acid (40 uM) for 24 hours

first: Hewei

last: Zhang

first: Lijun

last: Kong

first: Cheng

last: Wang

first: Linxiao


title: Bulk RNA Sequencing of 86 Human Donor Lungs

city: San Francisco

first: Seoyeon

last: Lee

address: 513 Parnassus Ave HSE 1355B

department: Pulmonary and Critical Care Medicine

institute: University of California, San Francisco

summary: The goal of this study was to characterize the effect of age on gene expression in human lung. We collected distal lung samples from 86 human donors distributed in age between 16 and 76 years and extracted RNA for Illumina-based sequencing.

overall_design:
Lung mRNA profiles of 86 human donor lungs with age ranging from 16 to 76.

**The submitter declares that the raw data are available in dbGaP (phs002484.v1.p1) due to patient privacy concerns.**

first: Kaveh

last: Boostanpour

first: Michael

last: Matthay

first: Walter

last: Eckalbar

first: Paul

last: Wolters

first: Mallar

last: Bhattacharya


title: Single-cell genomics predict germinal centre-associated etiology of autoimmune risk loci

city: Stanford

first: Zohar

last: Shipony

address: Beckman Center B-279A  279 Campus Drive West

institute: Stanford University

summary: The germinal centre (GC) response is critical for both effective adaptive immune responses and establishing peripheral tolerance by limiting auto-reactive B cells. To understand the gene regulatory principles underlying B cell maturation and the GC response we generated a single-cell transcriptomic and epigenomic atlas of the human tonsil, a widely studied, representative lymphoid tissue. We identify diverse immune cell subsets to help us map dynamic transcription factor activity during B cell activation, GC formation and plasma cell differentiation. We subsequently leverage cell type-specific transcriptomic and epigenomic maps to interpret the regulatory potential of fine-mapped autoimmune genetic variants. This reveals that many autoimmune disease-associated variants exhibit the greatest regulatory potential in GC-associated immune cell populations, providing a valuable cell-type resolved resource to understanding cellular and genetic causes underpinning autoimmune disease.

overall_design: Tonsil samples were collected from children and adults undergoing routine tonsillectomy. Tonsillar immune cells were loaded on to the 10X Genomics Chromium according to the manufacturer’s protocol using either the single-cell 3' kit (vX) or the single-cell ATAC kit (v1). Library preparation for both assays was performed according to the manufacturer’s protocol prior to sequencing on either the Illumina NovaSeq 6000 or NextSeq 500 platforms.

first: Hamish

middle: W

last: King

first: Kristen

last: Wells


title: EHEC MavR transcriptome and targetome

city: Charlottesville

first: Melissa

last: Kendall

state: VA

address: 1340 Jefferson Park Ave.

department: Microbiology

institute: University of Virginia

summary: The first goal of the study was to identify genes differentially regulated by MavR in EHEC strain 86-24. The second goal was to identify direct targets of MavR through the MAPS protocol.

overall_design: Identify the transcriptome and targetome of MavR

first: Amber

middle: B

last: Sauder

middle: M


title: Lipid droplets protect human β-cells from lipotoxic-induced stress and cell identity changes

status: Public on Sep 15 2021

city: Nashville

first: Xin

last: Tong

state: TN

address: 2213 Garland Ave

institute: Vanderbilt University

summary: Free fatty acids (FFAs) are often stored in lipid droplet (LD) depots for eventual metabolic and/or synthetic use in many cell types, such a muscle, liver, and fat. In pancreatic islets, overt LD accumulation was detected in humans but not mice. LD buildup in islets was principally observed after roughly 11 years of age, increasing throughout adulthood under physiologic conditions, and also enriched in type 2 diabetes. To obtain insight into the role of LDs in human islet β cell function, the levels of a key LD scaffold protein, perilipin2 (PLIN2), were manipulated by lentiviral-mediated knock-down (KD) or over-expression (OE) in EndoCβH2-Cre cells, a human cell line with adult islet β-like properties. Glucose stimulated insulin secretion was blunted in PLIN2KD cells and improved in PLIN2OE cells. An unbiased transcriptomic analysis revealed that limiting LD formation induced effectors of endoplasmic reticulum (ER) stress that compromised the expression of critical β cell function and identity genes. These changes were essentially reversed by PLIN2OE or using the ER stress inhibitor, tauroursodeoxycholic acid. These results strongly suggest that LDs are essential for adult human islet β cell activity by preserving FFA homeostasis.

overall_design: Bulk RNAseq was performed in 3 groups of EndoCbH2-Cre cells: Sham, PLIN2 knockdown and PLIN2 overexpress. Each group includes 3 biological replicates.

first: Roland

last: Stein


title: NPC transcriptome disection

city: Montreal

first: Pierre

last: Bensidoun

state: Quebec

address: 4850 Avenue Hotel de ville

department: biochemistry

institute: ircm-universite de montreal

summary: We report  the ananlysis of polyAdenylated transcripts copurified with nuclear pore complexes in yeast S.cerevisae. We purified all NPCs and the 2 different types of pores (basket-containing and basket-less pores) and co-isolated their interactomes. The transcripts co-purified were polyA enriched and sequenced with Novaseq6000, and identified over 300X10^6 reads

overall_design: Examination of the transcript purified with yeast NPCs.

first: Taylor

last: Reiter

first: Ben

last: Montpetit

first: Daniel

last: Zenklusen

first: Marlene

last: Oeffinger


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [RNA-seq]

city: Hangzhou

first: Hua

last: Yu

address: No.18 Shilongshan Road

institute: Westlake University

summary: Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). When mES cells undergo rRNA biogenesis defect, the normal LLPS of nucleolus is disrupted, causing deconjugation of NCL/TRIM28 complex on PNH and changes of epigenetic state and 3D structure of PNH, which leads to Dux, a conserved multicopy retrogene defining the cleavage-specific transcriptional program in placental mammals, to be released from the PNH region, activation of 2C-like program and transition of mES cells to 2C-like cells. Embryos with rRNA biogenesis defect are incompatible to develop from 2-cell (2C) to blastocyte (BC) and appear to skew from the blastocyst to earlier cleavage embryo signatures. Our results highlight that nucleolar LLPS-mediated 3D chromatin structure reshaping of PNH compartment regulates the fate transition of mES cells to 2C-like cells. Our findings for the first time elucidate the novel roles of rRNA biogenesis in regulating the 2C-like and ES state homeostasis in cultured cells and suggest that rRNA biogenesis is a new molecular switch from nucleolus-unmatured 2C stage to nucleolus-matured BC stage during murine pre-implantation embryo development.

overall_design: Examination of gene expression in control and CX-5461 treated ES and mouse embryo.

first: Zhen

last: Sun


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [Hi-C]

overall_design: Examination of the difference of chromatin high-order structure in control ES cells and CX-5461 treated ES cells.


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [ChIP-seq]

overall_design: Examination of histone modifications and NCL/TRIM28 binding in control and CX-5461 treated ES cells by ChIP-seq.


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [ATAC-seq]

overall_design: Examination of the difference of chromatin openness in mouse ES cells.


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin

summary: This SuperSeries is composed of the SubSeries listed below.


title: Cell size is a determinant of stem cell potential during aging (HSC size-fractionation RNA-seq dataset)

first: Charles

last: Whittaker

overall_design: Two replicates each of RNA isolated from small (XS-HSCs), medium (M-HSCs) and large (XL-HSCs) hematopoetic stem cells. Four replicates each of RNA isolated from Hematopoetic Stem Cells isolated from mice treated with vehicle, PD, rapamycin and PD+rapamycin.

first: Jette

last: Lengefeld

first: Chia-Wei

last: Cheng

first: Pema

last: Maretich

first: Marguerite

last: Blair

first: Hannah

last: Hagen

first: Melanie

last: McReynolds

first: Emily

last: Sullivan

first: Kyra

last: Majors

first: Christina

last: Roberts

first: Joon

last: Kang

first: Joachim

last: Steiner

first: Teemu

last: Miettinen

first: Scott

last: Manalis

first: Adam

last: Antebi

first: Sean

middle: J

last: Morrison

first: Jacqueline

middle: A

last: Lees

first: Laurie

last: Boyer

first: Ömer

last: Yilmaz

first: Angelika

last: Amon


title: Transcriptome study of iPSC-CMs under biochemical and biomechanical maturation conditions

city: Ann Arbor

last: Helms

state: MI

address: 7220 MSRB3, 1150 W. Medical Center Dr., SPC 5644

department: Internal Medicine

institute: University of Michigan

summary: This analysis compared cardiomyocytes derived from induced pluripotent stem cells under biochemical and biomechanical conditions expected to induced maturation.

overall_design: Induced pluripotent stem cells were differentiated into cardiomyocytes, purified by metabolic selection, then cultured as either monolayers (ML) or as 2D cardiac muscle bundles (2DMBs, also referred to as M2Ds, or 2D-microtissues) under different media conditions expected to induce maturation.  All biologic replicates were derived from pooled iPSC-CMs from the same 3 batches to avoid batch-to-batch variability.


title: PD-L1 blockade-induced temporal single cell dynamics in triple negative breast cancer

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Yiheyuan Road

department: BIOPIC

institute: Peking Univerisity

summary: Despite the progress in immunotherapies, leading immune checkpoint inhibitors are only effective in a subset of patients. The efficacy of atezolizumab, an anti-PD-L1 antibody, in triple negative breast cancer (TNBC) is limited for unknown reasons. We utilized single-cell RNA- and ATAC-sequencing to examine the dynamics of immune cells in metastatic TNBC patients treated with paclitaxel or its combination with atezolizumab. We found that paclitaxel selectively damaged tumor-reactive T cells while atezolizumab was effective in a small set of patients with high levels of baseline B cells and CXCL13+ T cells. B cells concertedly expanded with CXCL13+ T cells in responsive patients following paclitaxel plus atezolizumab treatment. Our data highlight the importance of potential tumor-reactive T cells and their orchestrators in the effective response to anti-PD-L1 therapies, and reveal drawbacks of existing clinical trials for TNBC.

overall_design:
The mechanism underlying combination therapy of paclitaxel plus atezolizumab in advanced TNBC is poorly understood. Using single-cell RNA-seq and ATAC-seq technologies, we generated transcriptomes and chromatin accessibility profiles of CD45+ immune cells from primary or metastatic tumor tissues and peripheral blood of 22 advanced TNBC patients treated with paclitaxel or its combination with atezolizumab.Raw sequence data were provided at: China Genomic Sequence Archive (GSA), and we will provide the accession number once the paper is accepted.
Raw data will be uploaded to China Genomic Sequence Archive (GSA), according to the Regulations on the Management of Human Genetic Resources in China.

first: Hongyan

last: Chen

first: Xueda

last: Hu

first: Hongnan

last: Mo

first: Ranran

last: Gao

first: Binghe

last: Xu

first: Fei

last: Ma

first: Zemin

first: Zhihua

last: Liu


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [scRNA-seq]

first: Hua

last: Yu

overall_design: Examination of gene expression in control and CX-5461 treated ES cells in single-cell level.

first: Zhen

last: Sun


first: Tina

last: O'Grady

state: LA

summary: iCLIP of HeLa cells with anti-TFIP11 antibody to investigate RNA binding locations of TFIP11 as part of a larger study on the function of TFIP11.

overall_design: iCLIP of HeLa cells with anti-TFIP11 antibody. Two barcoded libraries (GGTT and TTGT) were used in the analysis.

first: Denis

last: Mottet

first: Amandine

last: Duchemin

first: Yann

last: Audic

first: Agnes

last: Méreau


title: RNA Expression Profiling Comparing ER+ Postpartum Breast Cancer with ER+ Nulliparous Breast Cancer

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Purpose: To perform RNA-Seq expression profiling from Young Women's Breast Cancer FFPE tissues, comparing ER+ Postpartum Brest Cancer to ER+ Nulliparous Breast Cancer
Methods:  RNA was extracted and isolated from archival Estrogen Receptor Positive primary breast cancer FFPE tissues ( 9 Postpartum, 7 Nulliparous). RNA species selected for inclusion in library utilzing Illumina-Access bead based oligo library preparation representing > 98% of known protein coding genes.
Results: We identified gene pathway differences in estrogen receptor signaling, t-cell immunity and cell cycle between nulliparous and postpartum breast cancer cases.  Subset analysis also revealed an enrichment in  extra-cellular matrix pathway related genes in postpartum compared to nulliparous and luminal A cases.

overall_design: FFPE derived mRNA from 9 Postpartum  and 7 Nulliparous Young Women's Breast Cancer cases generated by 100-cycle, single-ended, sequencing  of approxinately 70 million reads per sample using Illumina HiSeq 2500 sequencer.  Base call files were converted to fastq format using Bcl2Fastq.

first: Pepper

last: Schedin


title: single-cell sequencing of testis cells from Tex13a-Knockout mice versus wild-type mice

status: Public on Sep 14 2021

city: Nantong

first: Yinchuan

last: Li

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

institute: Nantong University

summary: To characterize the role of CCR4-NOT complex and Tex13a in late steps of spermiogenesis, Tex13a-Knockout mice were generated. To check the differential expression profile in elongating spermatids, scRNA-seq were adopted.

overall_design: All exons of Tex13a were knocked-out by CRISPR-CAS9 in C57BL/6 mice. Adult mice testes were pooled and digested with collagenase I and cell suspensions were then subjected to library preaparation. The libraries were sequenced on the Illumina HiSeq X using 150 bp paired end reads.


title: Integrative Epigenomic and High-Throughput Functional Enhancer Profiling Reveals Determinants of Enhancer Heterogeneity in Gastric Cancer

city: Singapore

first: TAOTAO

last: SHENG

address: 21 Lower Kent Ridge Rd, Singapore

country: Singapore

institute: NUS

summary: Enhancer variation has been proposed as a major cause of cancer heterogeneity – however, mechanisms driving patient-specific enhancer cartographies remain unclear. Here we applied microscale histone modification profiling to delineate the landscape of enhancers in primary gastric adenocarcinoma, analyzing 132 epigenomic profiles of primary tumors, normal tissues, and cell lines

overall_design: 28 GC cell lines, 4 gastric normal cells, 18 primary GCs and 18 matched normal gastric tissues are profiled in multiple number of chromatin marks and DNA methylation (5mC).

first: Taotao

last: Sheng

first: Shamaine Wei Ting

last: Ho

first: Patrick

last: Tan


title: Commensal-related changes in the epidermal barrier function lead to alterations in the benzo[a]pyrene metabolite profile and its distribution in 3D-skin

status: Public on Sep 13 2021

city: Berlin

first: Lisa

middle: Lotte

last: Lemoine

address: Max-Dohrnstraße 8-10

institute: German Federal Institute for Risk Assessment

summary:
Exposure to xenobiotics has repeatedly been associated with adverse health effects. While the majority of reported cases still relates to direct substance effects, there is increasing evidence that microbiome-dependent metabolism of xenobiotic substances likewise has direct adverse effects on the host. This can be due to microbial biotransformation of compounds, interaction between the microbiota and the host’s endogenous detoxification enzymes or altered xenobiotic bioavailability. Polycyclic aromatic hydrocarbons (PAH) such as Benzo[a]pyrene (B[a]P) are among the most abundant environmental pollutants and contaminants. Yet, effects of the skin microbiota on B[a]P absorption, metabolism and distribution in humans remain unclear.  Here, we demonstrate that skin microbiota do metabolize B[a]P on and in human skin in situ, using a recently developed commensalic skin model. In this model microbial metabolism leads to high concentrations, of known microbial B[a]P metabolites on the surface as well as in the epidermal layers. In contrast to what was observed for uncolonized skin, metabolite as well as B[a]P concentrations were subject to altered rates of skin penetration and diffusion, resulting in up to 58 % reduction of metabolites recovered from basal culture medium. The results indicate the reason for this altered behavior to be a microbial induced change of the epidermal barrier function. Compared to uncolonized models, commensal colonization led to strengthening of tight junctions (TJ) as well as increased epidermal differentiation in the form of increased expression of E-cadherin, K10, FLG and IVN. Concomitantly colonized models showed decreased formation and penetration of the ultimate carcinogen Benzo[a]pyrene-7, 8-dihydrodiol-9, 10-epoxide (BPDE), leading, in consequence, to fewer BPDE-DNA adducts formed. Befittingly, transcript and expression levels of key proteins for repairing environmentally induced DNA-damage such as XPC were also found to be reduced in the commensalic models, as was expression of B[a]P-associated cytochrome P450-dependent monooxygenases (CYPs) such as CYP1A1.
The results show that the microbiome can have significant effects on the toxicology of external chemical impacts. The respective effects rely on a complex interplay between microbial as well as host metabolism and microbe-host interactions all of which cannot be adequately assessed using single-system studies. Given the high species-specificity of such interactions adequate toxicological assessments should thus increasingly rely on complex human models wherever possible.

overall_design: A co-cultures of EpiDermFT™ (MatTek) skin tissue and two different skin isolates (M. luteus and P. oleovorans) treated with B[a]P were analyzed using the Affymetrix Human Clariom S. Array data was processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany). Biological duplicates were performed for controls and replicates for each treatment.

first: Dilan

last: Bayrambey

first: Alexander

last: Roloff

first: Christoph

last: Hutzler

first: Luch

last: Andreas

first: Tewes

last: Tralau


title: Immunophenotyping and transcriptional profiling of human plasmablasts in dengue.

city: New Delhi

first: Anmol

last: Chandele

state: Delhi

address: Aruna Asaf Ali Marg

institute: International Center for Genetic Engineering and Biotechnology

summary: Plasmablats are the key cell type involved in Antibody (Ab) production that massively expand in dengue. However, little is known about their molecular profile in dengue . We investigated the transcriptional profiles of plasmablasts from dengue patients. We found that in addition to Ab secretion, they overexpress several molecules related to endothelial interactions, homing to skin or mucosal tisues.  Additionally, there are hints for potential involvement in processes such as angiogenesis, leukocyte extravasation and vascular permeability. This is the fisrt detailed transcriptional analysis of plasmablast from dengue patients in India. We use flow cytometry to phenotype these cells and bulk RNA sequencing to analyze their transcriptinal profiles.

overall_design: Expression analysis of CD19+ CD20+ IgD+ CD71- CD27- CD38- naïve B cells (N) and CD19+/int CD20- IgD- CD71+ CD27+ CD38+ plasmablasts (PB) sorted from Dengue patients.

first: Murali

last: Kaja


title: Fetal Growth Restriction Impairs Hippocampal Neurogenesis and Cognition via Tet1 in Offspring

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

summary: Fetal growth restriction (FGR) increases the risk for impaired cognitive function later in life. However, the precise mechanisms remain elusive. Using dexamethasone-induced FGR and protein restriction-influenced FGR mouse models, we observed learning and memory deficits in adult FGR offspring. FGR induces decreased hippocampal neurogenesis from the early postnatal period to adulthood by reducing the proliferation of neural stem cells (NSCs). We further found a persistent decrease of Tet1 expression in hippocampal NSCs of FGR mice. Mechanistically, Tet1 downregulation results in hypermethylation of the Dll3 and Notch1 promoters and inhibition of Notch signaling, leading to reduced NSC proliferation. Overexpression of Tet1 activates Notch signaling, offsets the decline in neurogenesis, and enhances learning and memory abilities in FGR offspring. Our data indicate that a long-term decrease in Tet1/Notch signaling in hippocampal NSCs contributes to impaired neurogenesis following FGR and could serve as potential targets for the intervention of FGR-related cognitive disorders.

overall_design: The hippocampi were obtained from NS and IUGR male C57BL/6J mice at postnatal day 3 and week 8.

first: Wen

last: Chen

first: Cizhong

last: Jiang

first: Jiuhong

last: Kang


title: RNASeq of RNA from naïve B cells and T cell blasts from individuals with AIOLOS N160S mutation and healthy controls

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr

department: Dept. of Lab Medicine

institute: NIH Clinical Center

summary: RNA-seq was performed using RNA extracted from enriched T cell blasts (CD3 T cells were enriched from the T-cell blasts, purity >90%, Stemcell Technologies, 19051) or naïve B cells (purity >90%, Stemcell technologies, 19254) for the following study groups: healthy controls (HC, n=3-4) and patients with AIOLOS N160S (n=1 for naïve B cells [A.III.1] and n=2 for T cell blasts [A.II.2 and A.III.1]). Libraries were prepared using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel, which captures 20,802 genes (>95% of human RefSeq genes). RNA-seq was performed on the Illumina HiSeq 2500 (Illumina; AmpliSeq for Illumina/HiSeq 2500). Demultiplexed reads were mapped to the hg19 genome using the splice-aware aligner Tophat (Trapnell et al., 2009). Gene-level counts data were generated using the Rsubread feature counts a read summarization program that counts mapped reads for genomic features such as genes(Liao et al., 2019). Differential expression analysis was performed using R (v.3.5.3) and DESeq2 (v.1.22.2)(Love et al., 2014).

overall_design: RNA sequencing was performed using the AmpliSeq for Illumina Transcriptome Human Gene Expression panel anf the Illumina HiSeq 2500 analyzer. We analyzed RNA samples extracted from enriched T cell blasts and naïve B cells from healthy controls and patients with AIOLOS N160S mutations.

first: Sergio

last: Rosenzweig

first: Hyesun

last: Kuehn

first: Jennifer

last: Stoddard


title: Effects of ambient temperature on transcript levels and alternative polyadenylation in Drosophila melanogaster [RNA-seq]

city: Zurich

first: Christian

middle: F.

last: Lehner

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures.  However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation. To assess the effects of temperature change within the readily tolerated range on the transcriptome, we have performed analyses with the ectothermic organism Drosophila melanogaster. Both adult male flies and S2R+ cells were analyzed.  3' RNA-Seq was applied to study effects of ambient temperature change on transcript levels and on polyadenylation site selection.

overall_design: Aliquots of adult male flies and S2R+ cells, respectively, were shifted to distinct temperatures (11, 14, 25 and 30°C). Twenty-four hours later, total RNA was isolated and analyzed by 3' RNA-Seq. Three replicate experiments were performed.

first: Yu

last: Bai

first: Emmanuel

last: Caussinus

first: Gregor

last: Rot

middle: F


title: Ductal macrophages predominate in the immune landscape of the lactating mammary gland

city: Rouen

first: Chervin

last: Hassel

address: GRAM2.0 - EA2656 - UFR Santé - 22 Boulevard Gambetta - CS 76183 - 76183 ROUEN Cedex 1

department: UFR Santé

institute: Université de Rouen

summary: The mammary gland is unique in female mammals. Mammary tissue undergoes development and remodeling during lactation, a stage associated with high susceptibility to bacterial infections, inducing an inflammatory condition called mastitis. Although the immune response of the mammary gland has been the subject of intense research to improve prevention and treatment efficacy, the precise definition of its immune composition at this particular physiological stage is still missing. We combined single-cell RNA-Seq, flow cytometry, and three-dimensional confocal microscopy techniques to characterize the immune landscape of lactating murine mammary tissue. Macrophages dominated the immune cell repertoire and could be subdivided into at least two subsets: ductal and stromal macrophages. Ductal macrophages represented approximately 80% of the total CD45pos immune cells and co-expressed F4/80 and CD11c, with high levels of MHC class II molecules. They were strategically poised below the alveolar basal cells in contact with the myoepithelial cell network. Adaptive T and B lymphocytes were remarkably less numerous at this stage, which could explain the limited efficacy of vaccination against mastitis. These results support the view that new strategies to increase mammary immunity and prevent mastitis should be devised.

overall_design: Gene expression profiles of single lived resident immune cells from lactating mice mammary gland were generated using 10X Genomics Chromium platform.

first: Blandine

last: Gausserès

first: Laurence

last: Guzylack

first: Gilles

last: Foucras


title: Effects of ambient temperature on DNA accessibility in nuclear chromatin  of Drosophila S2R+ cells [ATAC-seq]

summary: Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures.  However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation, including the transcriptional level. To study effects of changes in ambient temperature on chromatin accessibility, we performed ATAC-Seq with S2R+ cells, a line derived from embryos of the ectothermic organism Drosophila melanogaster. Aliquots of S2R+ cells were exposed to different temperatures (14, 25 and 29°C) within the readily tolerated range before analysis with ATAC-Seq.

overall_design: Aliquots of S2R+ cells were plated and incubated for 36 hours at 25°C, followed by a shift to either 14, 25 or 29°C. Cells were harvested 24 hours after this temperature shift and processed for tagmentation, which was done at 25°C for all samples. Three replicate experiments were performed.

first: Stefano

last: Leo


title: Temporal dynamics of transcriptome change in Drosophila S2R+ cells after a temperature shift from 25 to 14°C

summary: Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures.  However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to distinct temperatures is predicted to involve complex regulation. To assess the effects of a temperature downshift from 25 to 14°C, i.e. from the optimal temperature to the lower limit of the readily tolerated range, on the transcriptome in a time-resolved manner, we have performed expression profiling with S2R+ cells, which are derived from the ectothermic organism Drosophila melanogaster.

overall_design: Aliquots of S2R+ cells were plated and incubated at 25°C for 36 hours before a temperature downshift shift to 14°C was applied. At 0, 4, 12, 24 and 72 hours after the temperature downshift, total RNA was isolated and processed for hybridization to microarrays. For control, an additional aliquot was maintained at 25°C for 12 hours rather than shifted to 14°C, resulting in a cell density comparable to that obtained after 72 hours at 14°C. The experiment was teplicated until at least three replicates of sufficient technical quality were available for each time point.


title: Effect of histone H2Av depletion on temperature dependence of the Drosophila S2R+ cell transcriptome

summary: The histone H2A variant H2A.Z has a crucial role in the regulation of temperature-dependent gene expression in the plant Arabidopsis thaliana. To evaluate whether the Drosophila homolog histone H2Av has a similar role in the control of the transcriptional response to temperature change, we depleted this histone variant by RNA interference in S2R+ cells and analyzed the effect on the transcriptome after temperature shifts to different temperatures (14, 25 and 30°C). For control, we performed analogous experiments using treatment with lacZ dsRNA instead of His2Av dsRNA.

overall_design: S2R+ cells were treated with either His2Av dsRNA or lacZ dsRNA at the optimal growth temperature (25°C) before shifting culture aliquots to different temperatures (14, 25 and 30°C). Twenty-four hours after the temperature shift, RNA was isolated and processed for hybridization to microarrays. Three replicate experiments were performed.

first: Fritz

last: Bosshardt


title: Temperature dependence of the transcriptome in cultured Drosophila S2R+ cells

summary: Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures.  However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation. To assess the effects of temperature change within the readily tolerated temperature range on the transcriptome, we have performed expression profiling with S2R+ cells, which are derived from the ectothermic organism Drosophila melanogaster.

overall_design: Aliquots of S2R+ cells were plated and shifted to different temperatures (11, 14, 25, and 30°C).  Twenty-four hours after the temperature shift, total RNA was isolated and processed for hybridization of microarrays. Three replicate experiments were preformed.


title: Effects of temperature change within the readily tolerated range on transcription and DNA accessibility in the Drosophila S2R+ cell line

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Inhibition of Bromodomain and Extra Terminal (BET) domain activity modulates the IL-23R/IL17 axis and suppresses acute Graft-Versus-Host Disease

status: Public on Sep 12 2021

city: Columbus

first: Parvathi

last: Ranganathan

state: Ohio

address: 460 W 12th Ave, BRT 420

department: Hematology

institute: The Ohio State Univeristy


title: Inhibition of Bromodomain and Extra Terminal (BET) domain activity modulates the IL-23R/IL17 axis and suppresses acute Graft-Versus-Host Disease [RNA-Seq]

summary: Acute graft-versus-host disease (GVHD) is the major cause of non-relapse mortality post-allogeneic stem cell transplantation. The majority of patients non-responsive to front line treatment with steroids have an estimated overall 2-year survival rate of only 10%. Treatment options for steroid-refractory acute GVHD are limited. Bromodomain and Extraterminal Domain (BET) inhibitors PLX51107 and PLX2853, deemed safe in human clinical trials in high risk malignancies, significantly downregulate pro-inflammatory Th1 and Th17 responses without impacting T regulatory cells, improving survival in murine models of acute GVHD while retaining beneficial graft-versus-leukemia effects.  Modulation of the IL23/STAT3 axis via BET inhibition resulted in a reduction of pathogenic Th1/Th17 cells in the spleen and acute GVHD target organs such as the gastrointestinal tract.  Based on our preclinical data presented here, PLX51107 will enter clinical trial for refractory acute GVHD in a Phase 1 safety, biological efficacy trial.

overall_design: 8 samples; 4 control (DMSO) vs. 4 treated (PLX2)

first: Katiri

last: Snyder

first: Lotus

last: Neidemire-Colley

first: Hannah

last: Choe


title: Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease (ATAC_Treat)

status: Public on Sep 10 2021

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

summary: Lung diseases, such as cystic fibrosis and COPD, are characterized by mucus obstruction and chronic airway inflammation, but their mechanistic link remains poorly understood. Here, we focused on the role of the mucostatic airway microenvironment on epigenetic reprogramming of airway macrophages (AM) and resulting transcriptomic and phenotypical changes. Using a muco-obstructive mouse model (Scnn1b-transgenic), we identified epigenetically controlled, differentially regulated pathways and transcription factors involved in inflammatory responses and macrophage polarization. Ex vivo stimulation of wild-type AMs with mucus induced gene expression changes, comparable with those observed in AMs from Scnn1b-transgenic mice. Functionally, AMs from Scnn1b-transgenic mice displayed impaired efferocytosis, phagocytosis and excessive inflammatory responses upon lipopolysaccharide challenge, mediated through enhanced Irf1 activity and expression. Our data show that mucostasis induces epigenetic reprogramming of AMs, leading to changes favoring tissue damage and disease progression. Targeting of these altered AMs may support therapeutic approaches in patients with muco-obstructive lung diseases.

overall_design: RNAseq, ATACseq and tWGBS was performed on wildtype as well as transgene airway macrophages. In addition RNAseq as well as ATACseq was performed on wildtype and transgene airway macrophages upon stimulation with medium or lipopolysaccharide for 12 hours.

first: Michelle

last: Paulsen


title: Dichotomous metabolic networks govern human ILC2 proliferation and function

city: Paris

first: James

last: Di Santo

address: 28 Rue du Dr Roux

department: Immunology

institute: Institut Pasteur

summary: Group 2 innate lymphoid cells (ILC2) represent innate homologues of Th2 cells that participate in immune defense and tissue homeostasis through production of type 2 cytokines. While T lymphocytes metabolically adapt to microenvironmental changes, knowledge of human ILC2 metabolism is limited and its key regulators are unknown. Here we show that circulating “naïve” ILC2 have an unexpected metabolic profile with a higher level of oxidative phosphorylation (OXPHOS) than NK cells. Accordingly, ILC2 are severely reduced in patients with mitochondrial disease and impaired OXPHOS. Metabolomic and nutrient receptors analysis reveals ILC2 uptake amino acids to sustain OXPHOS at steady-state. Upon activation with interleukin 33 (IL-33), ILC2 become highly proliferative relying on glycolysis and mTOR to produce IL-13, while continuing to fuel OXPHOS with amino acids to maintain cellular fitness and proliferation. Our results suggest that proliferation and function are metabolically uncoupled in human ILC2, offering new strategies to target ILC2 in disease settings.

overall_design: CRTh2+ ILC2 and CD56Dim NK cells were freshly isolated by FACS from peripheral blood of three healthy adult individuals. In total, 6 samples were analyzed and comparing between two cell populations.

first: J

first: I

last: Amit

first: L

last: Surace


title: Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease (RNA_Treat)


title: Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease (RNA_BL)


title: Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease (WGBS_BL)


title: Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease


title: Intra- and inter-tumoral heterogeneity of liver metastases in a patient with uveal melanoma

city: Joondalup

first: Elin

last: Gray

state: Western Australia

address: 270 Joondalup Drive

department: School of Medical and Health Sciences

country: Australia

institute: Edith Cowan University

summary: Tumour heterogeneity has been the main obstacle to the clinical efficacy of targeted and immunotherapy in cancer. An accurate understanding and recognition of tumour heterogeneity is critical in the clinical management of cancer patients. Here, we utilised single-cell RNA sequencing (scRNA-seq) to uncover the intra- and inter-tumoural heterogeneity of liver metastases from a patient with metastatic uveal melanoma.

overall_design: Single-cell RNA sequencing was performed on two liver metastases from a patient with uveal melanoma

first: Weitao

last: Lin

first: Aaron

last: Beasley

first: Nima

last: Ardakani

first: Elena

last: Denisenko

first: Leslie

last: Calapre

first: Matthew

last: Jones

first: Benjamin

last: Wood

first: Lydia

last: Warburton

first: Alistair

last: Forrest

middle: S


title: Phase II Study of Immune Checkpoint Blockade with Pembrolizumab after High Dose Cytarabine in Relapsed/Refractory Acute Myeloid Leukemia

status: Public on Sep 09 2021

city: Chapel Hill

first: Jonathan

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

summary: To address the role of immune dysregulation in AML, we conducted a phase II study of high-dose cytarabine followed by pembrolizumab 200 mg IV on day 14 to examine whether programmed death-1 inhibition improves clinical responses in relapsed/refractory (R/R) AML. Overall responders could receive pembrolizumab maintenance up to two years. Among thirty-seven patients enrolled, the overall response rate, composite complete remission rate (CRc; primary endpoint), and median overall survival (OS) were 46%, 38% and 11.1 months, respectively. Patients with refractory/early relapse and those receiving treatment as first salvage had encouraging outcomes (median OS 13.2 and 11.3 months, respectively). Grade >3 immune-related adverse events were rare (14%) and self-limiting. Patients who achieved CRc had a higher frequency of progenitor exhausted CD8+ T-cells in the bone marrow prior to treatment and a non-significant increase in baseline T-cell diversity.

overall_design:
The primary objective of this single-arm open-label phase II study was to estimate the composite CR (CRc: CR + CRi) rate of HiDAC followed by pembrolizumab in R/R AML. The study design was a Simon’s like two-stage design with relaxed stopping for futility. Relaxed stopping refers to inclusion of PR in the first stage as some of these PRs may convert to a CR during maintenance phase. The null hypothesis that the true CRc rate for HiDAC followed by pembrolizumab is 20% was tested against a one-sided alternative hypothesis. In the first stage, 19 patients were enrolled. If the number of patients who achieved a CRc plus the number of patients with PR was equal to <4 in these 19 patients, the study would be stopped for futility. Otherwise, 18 additional patients were enrolled for a total of 37 patients. The null hypothesis will be rejected if  >12 CRc’s are observed in 37 patients. Assuming that the PR rate has a uniform distribution, this design yields a type 1 error rate of at most 5% and power of at least 84% when the true CR rate for HiDAC followed by pembrolizumab is 40%. Secondary endpoints of this study included rates of unacceptable toxicity as defined in Safety Assessment, toxicity of HiDAC + pembrolizumab induction phase and pembrolizumab maintenance, objective overall response rates (ORR: CR + CRi + PR + MLFS), OS defined as day 1 of treatment until date of last known follow-up, relapse-free survival (RFS) defined as time from CRc until relapse or death, progression-free survival (PFS) defined as time from ORR until relapse, progression, or death, and event-free survival (EFS) defined as day 1 of treatment until no response, relapse or death. Survival measurements were summarized by Kaplan-Meier methodology.

** Submitters declare that they do not have consent to deposit the raw data in GEO and the raw data will be made available through the University of North Carolina at Chapel Hill (UNC) **

first: Joshua

last: Zeidner

middle: G

last: Vincent

first: Anastasia

last: Ivanova

first: Dominic

last: Moore

first: Karen

last: McKinnon

first: Alec

last: Wilkinson

first: Rupkatha

last: Mukhopadhyay

first: Francesco

last: Mazziotta

first: Hanna

last: Knaus

middle: C

last: Foster

first: Catherine

last: Coombs

first: Katarzyna

last: Jamieson

first: Hendrik

last: Van Deventer

last: Webster

first: Gabrielle

last: Prince

first: Amy

last: DeZern

first: B

middle: D

last: Smith

first: Mark

last: Lewis

first: Nathan

last: Montgomery

first: Leo

last: Luznik

first: Ivana

last: Gojo


title: Gene expression signatures of A2058 cells treated with neopetasin, metformin, and phenformin

city: Gifu

first: Kazuki

last: Heishima

address: Yanagido 1-1

country: Japan

institute: Gifu University

summary: To examine the difference of gene expression profiles between malignant melanoma cells treated with neopetasin (NP), metformin (Met), and phenformin (Phen), we have employed microarray expression profiling as a discovery platform. A2058 (human malignant melanoma) cells were treated for 8 hours with NP (3 µM), Met (5,00 µM), and Phen (50 µM).

overall_design: Gene expression in a human malignant melanoma cell line (A2058) treated with NP, Met, and Phen was measured at 8 hours after exposure to doses of 3, 5000, 50 µM of NP, Met, and Phen, respectively. Due to different solvent employed for each compound, profiles of the cells treated with NP was compared to that of DMSO; and, the profiles of the cells treated with Met and Phen were compared to that of water. Three independent experiments were performed.


title: NTRC controls chloroplast redox homeostasis through the regulation of the redox balance of 2-Cys Prxs in Arabidopsis

city: Seville

first: Francisco

middle: Javier

last: Cejudo

state: Seville

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

institute: University of Sevilla

summary: Thiol-dependent redox regulation is essential for the rapid adaptation of chloroplast metabolism to unpredictable changes of light intensity. The disulfide reductase activity of thioredoxins (Trxs), which relies on photo-reduced ferredoxin (Fdx) and a Fdx-dependent Trx reductase (FTR), constitutes the Fdx-FTR-Trxs system, which links chloroplast redox regulation to light. In addition, chloroplasts harbor an NADPH-dependent Trx reductase (NTR) with a joint Trx domain, NTRC. The activity of these two redox systems is integrated by the balance of the hydrogen peroxide scavenging enzyme 2-Cys peroxiredoxin (2-Cys Prx), which thus plays a key role in maintaining the reducing capacity of chloroplast Trxs in response to light intensity. Based on the severe phenotype of mutant lines lacking NTRC, it is clear that this enzyme plays an essential role in chloroplast redox homeostasis. However, whether the function of NTRC depends on its capacity of reduce 2-Cys Prxs or has additional targets remains unknown. Here, we have addressed this issue by a comparative analysis of the triple mutant of Arabidopsis thaliana, ntrc-2cpab, simultaneously lacking 2-Cys Prxs and NTRC, and the double mutant 2cpab lacking 2-Cys Prxs. The phenotype of the ntrc-2cpab mutant is indistinguishable of the 2cpab mutant, as shown by growth rate, photosynthesis performance, light-dependent redox regulation of enzyme activity and comparative transcriptomics based RNA-Seq. Based on these results, we propose that the function of NTRC in chloroplast redox homeostasis is exerted by the regulation of the redox balance of 2-Cys Prxs rather than by the direct reduction of additional targets.

overall_design: Eight-week-old short-day grown wild-type, 2cpab and ntrc-2cpab plants were randomly selected and young rosette leaves collected  after  2  hours  of  illumination  at  125  μE  m-2 s-1.  Our  experimental  design consisted of three biological replicates for each genotype, each of them containing leaves from three individual plants


title: Short and long read sequencing of human mammary epithelial MCF10a-Snail-ER cells after Epithelial-to-Mesenchymal Transition initiation

city: Montpellier

first: Lucile

last: Broseus

address: 141, rue de la Cardonille

institute: CNRS

summary: We cultured MCF10a-Snail-ER cells and induced EMT initiation with tamoxifen. A matched sequencing of their PolyA RNA was performed, using Illumina and direct RNA Oxford Nanopore sequencing technologies. Both generated datasets supported the development of hybrid bioinformatics tools.

overall_design: Parallel sequencing of matched MCF10a-Snail-ER PolyA RNA samples using Illumina and direct RNA Oxford Nanopore technologies.

first: Dany

last: Severac

first: Andrew

last: Oldfield

first: Emeric

last: Dubois

first: William

last: Ritchie


title: Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

overall_design: Two gene expression analysis experiments where various numbers of replicates of yeast cells expressing SARS-Cov2 receptor binding domain (RBD) transgenes were compared to cells expressing the P8 control transgene. The exp020821 experiment compares wild type or engineered RBD to controls. The exp031020 compares wild type RBD to controls.

first: Neil

last: Dalvie

first: Sergio

last: Rodriguez-Aponte

first: Brittany

middle: L

last: Hartwell

first: Lisa

middle: H

last: Tostanoski

last: Biedermann

first: Laura

last: Crowell

first: Kawaljit

last: Kaur

first: Ozan

last: Kumru

first: Lauren

last: Carter

first: Jingyou

last: Yu

first: Aiquan

last: Chang

first: Katherine

last: McMahan

first: Thomas

last: Courant

first: Celia

last: Lebas

first: Ashley

last: Lemnios

first: Kristen

last: Rodrigues

first: Murillo

last: Silva

first: Ryan

last: Johnston

first: Christopher

last: Naranjo

first: Mary

last: Tracey

first: Joseph

middle: R

last: Brady

first: Dongsoo

last: Yun

first: Swagata

last: Kar

first: Maciel

last: Porto

first: Megan

last: Lok

first: Hanne

last: Andersen

first: Kerry

last: Love

first: Danielle

last: Camp

first: Judith

last: Silverman

first: Harry

last: Kleanthous

first: Sangeeta

last: Joshi

first: David

last: Volkin

first: Patrice

first: Nicolas


title: Epigenetic reprogramming of airway macrophages drives polarization and inflammation in muco-obstructive lung disease (ATAC_BL)

first: Joschka

last: Hey

first: Michelle

last: Paulsen


title: miR-33b-3p Suppresses Metastasis in Prostate Cancer by Targeting DOCK4

status: Public on Sep 08 2021

city: Harbin

first: Yu

last: Mei

address: 92 West Dazhi Street,Nan Gang District

institute: Harbin Institute of Technology

summary: Purpose: Despite that androgen-deprivation therapy results in long-lasting responses, the disease inevitably progresses to metastatic castration-resistant prostate cancer. In this study, we identified miR-33b-3p as a suppressor of metastasis in prostate cancer. miR-33b-3p was significantly reduced in prostate cancer tissues, and the low expression of miR-33b-3p was correlated with poor overall survival of prostate cancer patients. Overexpression of miR-33b-3p inhibited both migration and invasion of highly metastatic prostate cancer cells whereas antagonizing miR-33b-3p promoted those processes in lowly metastatic cells. The in vivo results demonstrate that miR-33b-3p suppresses metastasis of tail vein inoculated prostate cancer cells to lung, liver, and lymph node in mice. DOCK4 was validated as the direct target of miR-33b-3p. miR-33b-3p decreased the expression of DOCK4 and restoration of DOCK4 could rescue miR-33b-3p inhibition on cell migration and invasion. Moreover, downregulation of miR-33b-3p was induced by bortezomib, the clinically used proteasome inhibitor, and overexpression of miR-33b-3p rescued the insufficient inhibition of bortezomib on migration and invasion in prostate cancer cells. Collectively, our findings demonstrate that miR-33b-3p suppresses metastasis by targeting DOCK4 in prostate cancer. Our results suggest that enhancing miR-33b-3p expression may provide a promising therapeutic strategy for overcoming that proteasome inhibitor’s poor efficacy against metastatic prostate cancer.

overall_design: Mimic-negative control (NC) and mimic-miR-33b-3p (3p) were generated by deep sequencing,  using Illumina GAIIx.

first: Huanjie

last: Yang


title: A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress [ChIP-seq]

first: romain

last: forey

address: 142 avenue de la Cardonille

institute: IGH

summary: Upon replication stress, the Mec1ATR kinase triggers the downregulation of transcription, reducing the level of RNA polymerase on chromatin to facilitate replication fork progression. We identify a hydroxyurea-induced phosphorylation site at Mec1-S1991 that contributes to the eviction of RNAPII and RNAPIII during replication stress. The non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. This defect can be suppressed by destabilizing chromatin-bound RNAPII with a Rpb3-TAP fusion, suggesting that lethality arises from replication-transcription conflicts. Coincident with a failure to repress gene expression, highly transcribed genes like GAL1 persist at nuclear pores in mec1-S1991A cells. Consistently, we find pore proteins and several components controlling RNAPII and RNAPIII transcription are phosphorylated in a Mec1-dependent manner, suggesting that Mec1-S1991 phosphorylation limits conflicts between replication and either RNA polymerase complex. We further show that Mec1 contributes to reduced RNAPII occupancy on chromatin during an unperturbed S phase.

overall_design: Pol2 genome-wide profiling during DNA replication stress in wt-cells and mec1 mutants

first: Felix

last: Jonas

first: Naama

last: Barkai


title: RNAseq of rabbit lungs infected with Mycobacterium tuberculosis as single cells or aggregates

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren St, Rm# W250.Q

department: New Jersey Medical School,

institute: Rutgers Biomedical and Health Sciences, Rutgers The State University of NJ

summary: The virulence of Mycobacterium tuberculosis (Mtb), either as mostly aggregates or single cells (Mtb-SC), was compared using a rabbit model of pulmonary infection. Our hypothesis is that aggregation contributes to enhanced virulence of Mtb. Rabbit lung transcriptome was analyzed by RNAseq to identify differentially regulated gene networks and pathways between Mtb-AG and Mtb-SC infection of rabbit lungs soon after seeding of the bacteria (24 hours post-inoculation).

overall_design: Lung mRNA profiles of adult New Zealand White rabbits infected with Mycobacterium tuberculosis as single cells or aggregates for 24 hours.


title: A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress [tDNA]

overall_design: Analysis of tDNA expression by strand specific, total RNA-seq of exponentially growing and HU-treated S. cerevisiae cells, wild type and mec1-S1991A mutant

first: Verena

last: Hurst

first: Kiran

last: Challa

first: Romain

last: Forey

first: Christoph

last: Schmid

first: Kenji

last: Shimada

first: Susan

last: Gasser

first: Jérôme

last: Poli


title: A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress

type: Genome variation profiling by high throughput sequencing